Baseline correction
A common framework with implementations of several baseline correction methods
| Package: | baseline |
| Type: | Package |
| Version: | 1.2-2 |
| Date: | 2019-11-05 |
| License: | GPL-2 |
Use function baseline for baseline correction. This function takes matrices of spectra, a method name and parameters needed for the specific method. See helpfiles for details.
Kristian Hovde Liland and Bjørn-Helge Mevik
Maintainer: Kristian Hovde Liland <kristian.liland@nmbu.no>
Andreas F. Ruckstuhl, Matthew P. Jacobson, Robert W. Field, James A. Dodd: Baseline subtraction using robust local regression estimation; CHAD A. LIEBER and ANITA MAHADEVAN-JANSEN: Automated Method for Subtraction of Fluorescence from Biological Raman Spectra; Mark S. Friedrichs: A model-free algorithm for the removal of baseline artifacts; AHMET K. ATAKAN, W. E. BLASS, and D. E. JENNINGS: Elimination of Baseline Variations from a Recorded Spectrum by Ultra-low Frequency Filtering; M.A. Kneen, H.J. Annegarn: Algorithm for fitting XRF, SEM and PIXE X-ray spectra backgrounds; K.H. Liland, B.-H. Mevik, E.-O. Rukke, T. Almøy, M. Skaugen and T. Isaksson (2009) Quantitative whole spectrum analysis with MALDI-TOF MS, Part I: Measurement optimisation. Chemometrics and Intelligent Laboratory Systems, 96(2), 210–218.
# Load data data(milk) # The baseline() function is an S4 wrapper for all the different # baseline correction methods. The default correction method # is IRLS. Data must be organized as row vectors in a matrix # or data.frame. bc.irls <- baseline(milk$spectra[1,, drop=FALSE]) ## Not run: # Computationally heavy plot(bc.irls) ## End(Not run) # Available extractors are: # getBaseline(bc.irls) # getSpectra(bc.irls) # getCorrected(bc.irls) # getCall(bc.irls) # Correction methods and parameters can be specified through the wrapper. bc.fillPeaks <- baseline(milk$spectra[1,, drop=FALSE], lambda=6, hwi=50, it=10, int=2000, method='fillPeaks') ## Not run: # Computationally heavy plot(bc.fillPeaks) ## End(Not run) # If a suitable gWidgets2 implementation is installed, a # graphical user interface is available for interactive # parameter adaption. ## Not run: # Dependent on external software baselineGUI(milk$spectra) ## End(Not run)
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